feat: fix MCP/API intelligence, add Neo4j persistence, enhance UI dashboard

Major improvements to the code intelligence pipeline:

- Fix getDetailedStats to use StatsService for rich categorized stats
  (was returning hardcoded empty maps for frameworks/infra/connections/auth)
- Fix findRelatedEndpoints to actually traverse graph for connected endpoints
- Fix readFile to return JSON errors consistently with other MCP tools
- Fix Neo4j label serialization bug (was returning count instead of names)
- Add Cypher-based bulkSave() to GraphStore for reliable Neo4j persistence
- Wire POST /api/analyze to persist analysis results to Neo4j + evict caches
- Attach edges to source nodes in Analyzer for downstream consumers
- Fix Quarkus/Micronaut detectors to require framework-specific imports
- Add ENTITY and 8 other node kinds to LayerClassifier backend classification
- Restore node properties from Neo4j prop_* prefixed keys on read
- Fix edge hydration in findAll(), findById(), findEdgesPaginated()
- Enhance UI dashboard with rich stats: languages, frameworks, infra, connections
- Add edge labels and layer badges to node detail panel

E2E validated against spring-petclinic: 719 nodes, 1396 edges, 21 REST endpoints
Tests: 1308 pass, 0 failures (up from 1298, +10 new tests)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: aksOps

src/main/java/io/github/randomcodespace/iq/analyzer/AnalysisResult.java

@@ -1,6 +1,9 @@
 package io.github.randomcodespace.iq.analyzer;
 
+import io.github.randomcodespace.iq.model.CodeNode;
+
 import java.time.Duration;
+import java.util.List;
 import java.util.Map;
 
 /**
@@ -14,6 +17,7 @@
  * @param nodeBreakdown       count of nodes per NodeKind value
  * @param frameworkBreakdown  count of nodes per detected framework
  * @param elapsed             wall-clock duration of the analysis
+ * @param nodes               the actual graph nodes (may be null for backward compat)
  */
 public record AnalysisResult(
         int totalFiles,
@@ -24,5 +28,17 @@ public record AnalysisResult(
         Map<String, Integer> nodeBreakdown,
         Map<String, Integer> edgeBreakdown,
         Map<String, Integer> frameworkBreakdown,
-        Duration elapsed
-) {}
+        Duration elapsed,
+        List<CodeNode> nodes
+) {
+    /** Backward-compatible constructor without nodes. */
+    public AnalysisResult(
+            int totalFiles, int filesAnalyzed, int nodeCount, int edgeCount,
+            Map<String, Integer> languageBreakdown, Map<String, Integer> nodeBreakdown,
+            Map<String, Integer> edgeBreakdown, Map<String, Integer> frameworkBreakdown,
+            Duration elapsed) {
+        this(totalFiles, filesAnalyzed, nodeCount, edgeCount,
+                languageBreakdown, nodeBreakdown, edgeBreakdown, frameworkBreakdown,
+                elapsed, null);
+    }
+}

src/main/java/io/github/randomcodespace/iq/analyzer/Analyzer.java

@@ -333,14 +333,26 @@ private AnalysisResult runWithCache(Path root, Integer parallelism, AnalysisCach
             }
         }
 
-        // 6. Compute node breakdown
+        // 6. Attach edges to their source nodes for downstream consumers
+        Map<String, CodeNode> nodeById = new HashMap<>(allNodes.size());
+        for (CodeNode node : allNodes) {
+            nodeById.put(node.getId(), node);
+        }
+        for (var edge : builder.getEdges()) {
+            CodeNode source = nodeById.get(edge.getSourceId());
+            if (source != null) {
+                source.getEdges().add(edge);
+            }
+        }
+
+        // 7. Compute node breakdown
         Map<String, Integer> nodeBreakdown = new HashMap<>();
         for (CodeNode node : allNodes) {
             String kindValue = node.getKind().getValue();
             nodeBreakdown.merge(kindValue, 1, Integer::sum);
         }
 
-        // 7. Compute edge breakdown
+        // 8. Compute edge breakdown
         Map<String, Integer> edgeBreakdown = new HashMap<>();
         for (var edge : builder.getEdges()) {
             String kindValue = edge.getKind().getValue();
@@ -383,7 +395,8 @@ private AnalysisResult runWithCache(Path root, Integer parallelism, AnalysisCach
                 nodeBreakdown,
                 edgeBreakdown,
                 frameworkBreakdown,
-                elapsed
+                elapsed,
+                allNodes
         );
     }
 

src/main/java/io/github/randomcodespace/iq/analyzer/LayerClassifier.java

@@ -24,7 +24,11 @@ public class LayerClassifier {
 
     private static final Set<NodeKind> BACKEND_NODE_KINDS = Set.of(
             NodeKind.GUARD, NodeKind.MIDDLEWARE, NodeKind.ENDPOINT,
-            NodeKind.REPOSITORY, NodeKind.DATABASE_CONNECTION, NodeKind.QUERY
+            NodeKind.REPOSITORY, NodeKind.DATABASE_CONNECTION, NodeKind.QUERY,
+            NodeKind.ENTITY, NodeKind.MIGRATION, NodeKind.SERVICE,
+            NodeKind.TOPIC, NodeKind.QUEUE, NodeKind.EVENT,
+            NodeKind.MESSAGE_QUEUE, NodeKind.RMI_INTERFACE,
+            NodeKind.WEBSOCKET_ENDPOINT
     );
 
     private static final Set<NodeKind> INFRA_NODE_KINDS = Set.of(
@@ -36,7 +40,8 @@ public class LayerClassifier {
     );
 
     private static final Set<NodeKind> SHARED_NODE_KINDS = Set.of(
-            NodeKind.CONFIG_FILE, NodeKind.CONFIG_KEY, NodeKind.CONFIG_DEFINITION
+            NodeKind.CONFIG_FILE, NodeKind.CONFIG_KEY, NodeKind.CONFIG_DEFINITION,
+            NodeKind.PROTOCOL_MESSAGE
     );
 
     private static final Pattern FRONTEND_PATH_RE = Pattern.compile(

src/main/java/io/github/randomcodespace/iq/api/GraphController.java

@@ -25,6 +25,9 @@
 import java.util.Map;
 import java.util.concurrent.atomic.AtomicBoolean;
 
+import io.github.randomcodespace.iq.graph.GraphStore;
+import org.springframework.cache.CacheManager;
+
 /**
  * REST API controller matching the Python OSSCodeIQ API paths.
  */
@@ -36,14 +39,20 @@ public class GraphController {
     private final QueryService queryService;
     private final Analyzer analyzer;
     private final CodeIqConfig config;
+    private final CacheManager cacheManager;
+    private final GraphStore graphStore;
     private final AtomicBoolean analysisRunning = new AtomicBoolean(false);
 
     public GraphController(@org.springframework.beans.factory.annotation.Autowired(required = false) QueryService queryService,
                            Analyzer analyzer,
-                           CodeIqConfig config) {
+                           CodeIqConfig config,
+                           @org.springframework.beans.factory.annotation.Autowired(required = false) CacheManager cacheManager,
+                           @org.springframework.beans.factory.annotation.Autowired(required = false) GraphStore graphStore) {
         this.queryService = queryService;
         this.analyzer = analyzer;
         this.config = config;
+        this.cacheManager = cacheManager;
+        this.graphStore = graphStore;
     }
 
     @GetMapping("/stats")
@@ -269,6 +278,19 @@ public ResponseEntity<?> triggerAnalysis(
         try {
             AnalysisResult result = analyzer.run(Path.of(config.getRootPath()), null);
 
+            // Persist to Neo4j if GraphStore is available
+            if (graphStore != null && result.nodes() != null && !result.nodes().isEmpty()) {
+                graphStore.bulkSave(result.nodes());
+            }
+
+            // Evict all Spring caches so queries pick up new data
+            if (cacheManager != null) {
+                cacheManager.getCacheNames().forEach(name -> {
+                    var cache = cacheManager.getCache(name);
+                    if (cache != null) cache.clear();
+                });
+            }
+
             Map<String, Object> response = new LinkedHashMap<>();
             response.put("status", "complete");
             response.put("total_files", result.totalFiles());

src/main/java/io/github/randomcodespace/iq/detector/java/MicronautDetector.java

@@ -55,6 +55,15 @@ public DetectorResult detect(DetectorContext ctx) {
         String text = ctx.content();
         if (text == null || text.isEmpty()) return DetectorResult.empty();
 
+        // First, require a Micronaut-specific indicator to avoid false positives on
+        // Spring Boot or other frameworks that share common annotations like
+        // @Controller, @Singleton, @Inject, @Scheduled, @EventListener, etc.
+        boolean hasMicronautIndicator = text.contains("io.micronaut")
+                || text.contains("@Client");
+        if (!hasMicronautIndicator) {
+            return DetectorResult.empty();
+        }
+
         if (!text.contains("@Controller") && !text.contains("@Get") && !text.contains("@Post")
                 && !text.contains("@Put") && !text.contains("@Delete")
                 && !text.contains("@Singleton") && !text.contains("@Prototype") && !text.contains("@Infrastructure")

src/main/java/io/github/randomcodespace/iq/detector/java/QuarkusDetector.java

@@ -49,6 +49,16 @@ public DetectorResult detect(DetectorContext ctx) {
         String text = ctx.content();
         if (text == null || text.isEmpty()) return DetectorResult.empty();
 
+        // First, require a Quarkus-specific indicator to avoid false positives on
+        // Spring Boot or other frameworks that share common annotations like
+        // @Transactional, @Scheduled, @Singleton, @ApplicationScoped, etc.
+        boolean hasQuarkusIndicator = text.contains("io.quarkus")
+                || text.contains("io.smallrye")
+                || text.contains("@QuarkusTest");
+        if (!hasQuarkusIndicator) {
+            return DetectorResult.empty();
+        }
+
         if (!text.contains("@QuarkusTest") && !text.contains("@ConfigProperty")
                 && !text.contains("@Singleton") && !text.contains("@ApplicationScoped")
                 && !text.contains("@RequestScoped") && !text.contains("@Scheduled")